GREMLIN Database
YDEB - Putative transcription factor YdeB
UniProt: P96659 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 153 (148)
Sequences: 1062 (730)
Seq/√Len: 60.0

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:
i j Sco Prob
31_Q50_S4.9411.00
144_I149_I3.9101.00
23_E30_K3.9001.00
145_T148_Q3.8421.00
66_L138_L3.5931.00
19_E37_R3.4961.00
22_E35_V3.4871.00
8_I57_I3.3411.00
23_E32_Q2.8381.00
62_D65_A2.7541.00
25_E30_K2.7121.00
15_A136_S2.3751.00
99_E102_E2.2881.00
66_L141_I2.2241.00
34_Y49_T2.0781.00
7_N17_I2.0741.00
84_W123_E1.9131.00
35_V46_M1.8951.00
24_K46_M1.8471.00
16_G36_I1.8431.00
84_W120_N1.8271.00
70_M74_Q1.7770.99
144_I148_Q1.7430.99
32_Q49_T1.7340.99
60_V141_I1.6520.99
94_K105_E1.6170.99
72_I101_Q1.5530.98
4_I20_A1.5530.98
13_H110_L1.5330.98
9_V15_A1.5150.98
94_K106_V1.4930.98
64_L68_H1.4430.98
120_N123_E1.3170.96
61_T100_I1.2980.95
67_K71_H1.2620.95
60_V140_V1.2150.93
97_T102_E1.2070.93
138_L149_I1.1930.93
86_Q122_S1.1860.93
7_N140_V1.1830.93
49_T52_I1.1790.92
61_T66_L1.1510.91
58_R100_I1.1460.91
91_N126_M1.1400.91
107_V130_A1.1380.91
72_I95_I1.1260.91
70_M149_I1.1250.91
80_R109_D1.1070.90
111_M127_L1.0960.89
105_E109_D1.0860.89
108_R122_S1.0800.89
34_Y57_I1.0800.89
58_R137_E1.0770.88
104_A138_L1.0740.88
65_A99_E1.0730.88
51_K55_S1.0490.87
51_K54_S1.0490.87
86_Q120_N1.0470.87
88_Y123_E1.0450.87
80_R83_P1.0430.87
2_F59_P1.0390.87
15_A118_A1.0310.86
85_K122_S1.0300.86
47_I55_S1.0230.86
18_I70_M1.0040.85
33_Y46_M1.0030.85
26_F56_N1.0010.85
83_P95_I0.9970.84
90_I93_D0.9880.84
104_A107_V0.9870.84
102_E105_E0.9860.84
15_A140_V0.9760.83
63_I141_I0.9660.82
8_I134_L0.9470.81
87_R98_G0.9470.81
61_T101_Q0.9360.80
63_I67_K0.9290.80
73_F104_A0.9270.80
5_G28_E0.9260.80
88_Y92_T0.9170.79
53_L72_I0.9070.78
143_G149_I0.9060.78
127_L131_Y0.9040.78
76_G95_I0.8920.77
19_E68_H0.8810.76
5_G17_I0.8780.76
88_Y125_K0.8760.76
15_A60_V0.8760.76
61_T65_A0.8710.75
104_A134_L0.8700.75
37_R42_N0.8610.74
83_P86_Q0.8450.73
3_Q32_Q0.8450.73
107_V134_L0.8380.72
131_Y135_I0.8370.72
83_P97_T0.8330.72
100_I134_L0.8320.72
11_P56_N0.8270.71
11_P98_G0.8240.71
65_A141_I0.8240.71
80_R87_R0.8200.71
93_D116_E0.8140.70
18_I34_Y0.8090.70
132_E146_E0.8020.69
3_Q21_I0.7980.69
63_I142_K0.7920.68
32_Q71_H0.7890.68
94_K97_T0.7740.66
145_T149_I0.7720.66
111_M135_I0.7590.65
84_W87_R0.7580.65
13_H120_N0.7510.64
110_L133_F0.7510.64
2_F83_P0.7490.64
76_G108_R0.7460.63
68_H101_Q0.7420.63
63_I68_H0.7410.63
59_P149_I0.7390.63
10_Y110_L0.7320.62
88_Y126_M0.7250.61
106_V124_K0.7240.61
66_L142_K0.7220.61
75_H108_R0.7170.60
11_P100_I0.7110.60
6_D147_K0.7100.60
113_M118_A0.7080.59
6_D139_E0.7060.59
45_V97_T0.7050.59
123_E126_M0.7030.59
36_I131_Y0.7030.59
15_A133_F0.7030.59
56_N124_K0.7000.59
65_A70_M0.6970.58
22_E46_M0.6960.58
88_Y91_N0.6900.57
64_L67_K0.6900.57
11_P16_G0.6860.57
72_I108_R0.6830.57
36_I52_I0.6820.57
53_L147_K0.6760.56
29_E59_P0.6750.56
115_K149_I0.6740.56
43_M98_G0.6710.55
3_Q65_A0.6710.55
29_E145_T0.6670.55
85_K88_Y0.6640.55
16_G38_M0.6620.54
84_W124_K0.6580.54
57_I121_A0.6570.54
18_I21_I0.6520.53
66_L149_I0.6490.53
81_L95_I0.6390.52
59_P143_G0.6390.52
103_G134_L0.6370.52
60_V89_K0.6340.51
87_R106_V0.6320.51
63_I145_T0.6290.51
68_H143_G0.6280.51
34_Y52_I0.6260.50
85_K120_N0.6230.50
84_W106_V0.6210.50
37_R44_T0.6190.50
49_T142_K0.6180.49
10_Y45_V0.6170.49
36_I47_I0.6130.49
106_V133_F0.6130.49
33_Y121_A0.6090.48
26_F124_K0.6080.48
13_H43_M0.6040.48
11_P47_I0.5980.47
15_A121_A0.5960.47
87_R110_L0.5900.46
113_M133_F0.5890.46
79_D112_R0.5870.46
106_V126_M0.5820.45
18_I36_I0.5800.45
92_T95_I0.5750.45
142_K149_I0.5720.44
3_Q49_T0.5700.44
114_K131_Y0.5670.44
83_P99_E0.5650.43
40_I132_E0.5640.43
5_G126_M0.5630.43
88_Y106_V0.5630.43
64_L69_I0.5620.43
44_T82_L0.5600.43
31_Q34_Y0.5570.43
23_E147_K0.5560.43
10_Y55_S0.5530.42
50_S59_P0.5520.42
7_N54_S0.5480.42
60_V103_G0.5480.42
42_N148_Q0.5480.42
83_P88_Y0.5450.41
118_A126_M0.5450.41
18_I133_F0.5450.41
107_V123_E0.5390.41
20_A49_T0.5360.40
43_M46_M0.5360.40
18_I62_D0.5340.40
3_Q68_H0.5310.40
69_I103_G0.5280.39
15_A40_I0.5260.39
74_Q148_Q0.5250.39
91_N134_L0.5250.39
45_V131_Y0.5230.39
52_I70_M0.5220.39
71_H147_K0.5210.39
11_P110_L0.5200.39
93_D117_K0.5180.38
32_Q143_G0.5180.38
12_M15_A0.5160.38
18_I37_R0.5160.38
45_V99_E0.5150.38
68_H71_H0.5120.38
55_S125_K0.5110.38
36_I73_F0.5090.37
69_I72_I0.5060.37
32_Q50_S0.5020.37
42_N121_A0.5000.37
111_M126_M0.5000.37
87_R120_N0.5000.37
Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

HHsearch Results:
Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.
PDB Chains Cov % HHΔ  
2lwjA 1 1 100 0.227 Contact Map
4kbmB 1 0.9281 100 0.234 Contact Map
4l5gA 1 1 100 0.263 Contact Map
2lt3A 1 0.6863 99.9 0.485 Contact Map
2lt4A 1 0.4248 99.8 0.606 Contact Map
2lt1A 1 0.4183 99.7 0.611 Contact Map
3mlqE 1 0.3072 99.6 0.647 Contact Map
2eyqA 1 0.8627 97.7 0.828 Contact Map
4c2tA 1 0 56.5 0.92 Contact Map
1pjrA 1 0 52.3 0.922 Contact Map

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

Page generated in 0.0066 seconds.